barcodesComparison.h

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#ifndef __LREZ_BARCODES_COMPARISON__
#define __LREZ_BARCODES_COMPARISON__
 
#include "utils.h"
#include "indexManagementBam.h"
 
struct hashPairs { 
    template <class T1, class T2> 
    size_t operator()(const pair<T1, T2>& p) const
    { 
        auto hash1 = hash<T1>{}(p.first); 
        auto hash2 = hash<T2>{}(p.second); 
        return hash1 ^ hash2; 
    } 
};
 
unsigned countCommonBarcodes(robin_hood::unordered_set<barcode> barcodes1, robin_hood::unordered_set<barcode> barcodes2);
 
robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> computePairwiseCommonBarcounts(robin_hood::unordered_map<string, robin_hood::unordered_set<barcode>> regionsBarcodes);
 
robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> compareRegions(string bamFile, string regions);
 
void computeCommonBarcodesCounts(robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs>& counts, BarcodesOffsetsIndex& BarcodesOffsetsIndex, BamReader& reader, const RefVector& rv, int size, string& qRegion);
 
robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> compareContig_BamReader(string bamFile, BarcodesOffsetsIndex& BarcodesOffsetsIndex, string contig, int size);
 
robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> compareContig(string bamFile, BarcodesOffsetsIndex& BarcodesOffsetsIndex, string contig, int size);
 
robin_hood::unordered_map<pair<string, string>, unsigned, hashPairs> compareContigs(string bamFile, BarcodesOffsetsIndex& BarcodesOffsetsIndex, string contigs, int size, unsigned nbThreads = 1);
 
#endif